FWIW, when I have experienced the same issue as the OP, I have assumed it to be seeing related or poor S/N ratio in my red zone location. Usually, starting over resulted in a better result.

My view of the polar region, however, is through a few tree branches, and one time recently windy conditions created the same problem. Under normal conditions with clear sky, I have found PoleMaster to work beautifully.

I have had this happen on my Mac. Usually it happens when I take too long between steps, so I try to do it as fast as possible. The software is not exactly bug free. If it does happen, I have to start over. Eventually it works like it is supposed to. I don't think it's seeing, because I can start over and it works just fine the second time. I think the program is just buggy. Most of the time, it works fine for me on the first time, as long as I go fast. I have done it with the mount on and tracking, and with the mount off. I personally don't see any difference, so I just leave the mount off and move it by hand.

This also happened to me - I bumped up the camera exposure a notch, and it seemed to fix it. Not sure if that was really the cause though. I hope the next version of the software is more like the method used in sharpcap 2.9. So much easier:)